High expression of SULF1 is associated with adverse prognosis in breast cancer brain metastasis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38590118", "kind": "science-record", "revision": 2, "content_hash": "sha256:1c019331eb5f8b2729fa0d342941997b0f7afc9f3e1406e7d153725ac56fe7f6", "created_at": "2026-11-01T19:20:33Z", "updated_at": "2026-11-01T21:32:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "High expression of SULF1 is associated with adverse prognosis in breast cancer brain metastasis.", "doi": "10.1002/ame2.12406", "pmid": "38590118", "authors": ["Yitong Li", "Tingting Feng", "Qinghong Wang", "Yue Wu", "Jue Wang", "Wenlong Zhang", "Qi Kong"], "journal": "Animal models and experimental medicine", "year": 2025, "abstract": "BACKGROUND: Breast cancer is the most common cancer in women, and in advanced stages, it often metastasizes to the brain. However, research on the biological mechanisms of breast cancer brain metastasis and potential therapeutic targets are limited.\nMETHODS: Differential gene expression analysis (DEGs) for the datasets GSE43837 and GSE125989 from the GEO database was performed using online analysis tools such as GEO2R and Sangerbox. Further investigation related to SULF1 was conducted using online databases such as Kaplan-Meier Plotter and cBioPortal. Thus, expression levels, variations, associations with HER2, biological processes, and pathways involving SULF1 could be analyzed using UALCAN, cBioPortal, GEPIA2, and LinkedOmics databases. Moreover, the sensitivity of SULF1 to existing drugs was explored using drug databases such as RNAactDrug and CADSP.\nRESULTS: High expression of SULF1 was associated with poor prognosis in advanced breast cancer brain metastasis and was positively correlated with the expression of HER2. In the metastatic breast cancer population, SULF1 ranked top among the 16 DEGs with the highest mutation rate, reaching 11%, primarily due to amplification. KEGG and GSEA analyses revealed that the genes co-expressed with SULF1 were positively enriched in the 'ECM-receptor interaction' gene set and negatively enriched in the 'Ribosome' gene set. Currently, docetaxel and vinorelbine can act as treatment options if the expression of SULF1 is high.\nCONCLUSIONS: This study, through bioinformatics analysis, unveiled SULF1 as a potential target for treating breast cancer brain metastasis (BM).", "claims": [{"id": "claim-method", "statement": "The GEO2R online analysis tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) detected the DEGs that were common to both primary BRCA and BM samples. The p value and |log2(fold change)| (|log2FC|) were calculated. Genes that meet the selection criteria, namely, a p value < 0.05 and |log2FC| ≥ 2, were considered DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38590118", "locator": "sections[4] \"Data processing of DEGs\" paragraph 2", "quote": "The GEO2R online analysis tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) detected the DEGs that were common to both primary BRCA and BM samples. The p value and |log2(fold change)| (|log2FC|) were calculated. Genes that meet the selection criteria, namely, a p value < 0.05 and |log2FC| ≥ 2, were considered DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data were retrieved and available online, and this research did not involve any experiments on humans or animals.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38590118", "locator": "sections[3] \"Public database analysis\" paragraph 2", "quote": "All the data were retrieved and available online, and this research did not involve any experiments on humans or animals."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In the metastatic breast cancer population, SULF1 ranked top among the 16 DEGs with the highest mutation rate, reaching 11%, primarily due to amplification.", "kind": "quantitative", "target": {"value": 11.0, "unit": "per cent", "tolerance": null, "source": "In the metastatic breast cancer population, SULF1 ranked top among the 16 DEGs with the highest mutation rate, reaching 11%, primarily due to amplification."}, "evidence": [{"asset": "source:pmid:38590118", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In the metastatic breast cancer population, SULF1 ranked top among the 16 DEGs with the highest mutation rate, reaching 11%, primarily due to amplification."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In the metastatic breast cancer population, SULF1 ranked top among the 16 DEGs with the highest mutation rate, reaching 11%, primarily due to amplification.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38590118"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE125989"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE125989"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38590118", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/ame2.12406", "sha256": "sha256:79ccb98b78dadab12cf88325f39503989065ccb662766498f08a648f1d4cdbf8", "bytes": 31254, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/ame2.12406", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11798736", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE125989", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE125989", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE125989", "version": null, "note": "All the data were retrieved and available online, and this research did not involve any experiments on humans or animals.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the data were retrieved and available online, and this research did not involve any experiments on humans or animals.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3587381", "GSM3587382", "GSM3587383", "GSM3587384", "GSM3587385", "GSM3587386", "GSM3587387", "GSM3587388", "GSM3587389", "GSM3587390", "GSM3587391", "GSM3587392", "GSM3587393", "GSM3587394", "GSM3587395", "GSM3587396", "GSM3587397", "GSM3587398", "GSM3587399", "GSM3587400", "GSM3587401", "GSM3587402", "GSM3587403", "GSM3587404", "GSM3587405", "GSM3587406", "GSM3587407", "GSM3587408", "GSM3587409", "GSM3587410", "GSM3587411", "GSM3587412"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Prinary breast cancers and brain metastasis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE43837", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43837", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE43837", "version": null, "note": "All the data were retrieved and available online, and this research did not involve any experiments on humans or animals.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All the data were retrieved and available online, and this research did not involve any experiments on humans or animals.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1071862", "GSM1071863", "GSM1071864", "GSM1071865", "GSM1071866", "GSM1071867", "GSM1071868", "GSM1071869", "GSM1071870", "GSM1071871", "GSM1071872", "GSM1071873", "GSM1071874", "GSM1071875", "GSM1071876", "GSM1071877", "GSM1071878", "GSM1071879", "GSM1071880", "GSM1071881", "GSM1071882", "GSM1071883", "GSM1071884", "GSM1071885", "GSM1071886", "GSM1071887", "GSM1071888", "GSM1071889", "GSM1071890", "GSM1071891", "GSM1071892", "GSM1071893", "GSM1071894", "GSM1071895", "GSM1071896", "GSM1071897", "GSM1071898", "GSM1071899"], "sample_count": 38, "group_sizes": null, "group_sizes_basis": null, "platform": "1352", "taxon": "Homo sapiens", "title": "A BRCA1 Deficient-Like Signature is Enriched in Breast Cancer Brain Metastases", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE125989 not downloaded", "asset:data:geo:GSE125989 licence not read", "asset:data:geo:GSE43837 not downloaded", "asset:data:geo:GSE43837 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-2", "family": "correlation_analysis", "specific": "spearman", "label": "Correlation analysis", "dsl_operations": ["spearman_rho"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Spearman correlation"}}, {"id": "method-3", "family": null, "specific": null, "label": "GEO2R differential gene expression analysis using p value and |log2(fold change)| criteria", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The GEO2R online analysis tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) detected the DEGs that were common to both primary BRCA and BM samples. 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